5-Hydroxytryptamine (serotonin, 5-HT) is a hormone and a neurotransmitter found in the central nervous system. The conformational flexibility of the alkyl side chains in 5-HT plays an important role in its binding to receptor sites. The FTIR spectra of 5-hydroxytryptamine in 14 solution and as a solid form were obtained in the range of 4000-400 cm(-1). Geometry optimization based on molecular mechanics (using MM + force field), semi-empirical quantum mechanical calculations (using AM1, PM3 and MINDO) and HF and B3LYP levels using the 321 G and 6-31 (d) basic sets were performed. The calculated geometric parameters were compared to the corresponding X-ray structure of 5-hydroxytryptamine. For the optimized structures by semi-empirical, ab initio and DFT calculations, vibrational spectra were also generated. The assignments of the observed bands corresponding to 5-HT were made on the basis of such calculation and the comparison with related molecules. (c) 2005 Elsevier B.V. All rights reserved.